Table of contents

Change of 'positionType'
Change of 'bpcCommentGroup'
Change of 'organism', 'organismType' and 'sourceDataType'
Changes for consistency
New event types 'protein splicing' and 'miscellaneous'

Not before: 02-Mar-2010

To allow the representation of evidences on individual sequence coordinates of RNA editing commments, we are going to add an optional evidence attribute to the XSD type positionType:

    <xs:complexType name="positionType">
        ...
        <xs:attribute name="evidence" type="xs:string" use="optional"/>
    </xs:complexType>

Not before: 02-Mar-2010

To allow the representation of evidences on biophysicochemical properties commments, we are going to modify the XSD type bpcCommentGroup by replacing all type="xs:string" by type="evidencedStringType":

    <xs:group name="bpcCommentGroup">
        <xs:sequence>
            <xs:element name="absorption" minOccurs="0" maxOccurs="1">
                <xs:complexType>
                    <xs:sequence>
                        <xs:element name="max" type="evidencedStringType" minOccurs="0" maxOccurs="1"/>
                        <xs:element name="text" type="evidencedStringType" minOccurs="0" maxOccurs="1"/>
                    </xs:sequence>
                </xs:complexType>
            </xs:element>
            <xs:element name="kinetics" minOccurs="0" maxOccurs="1">
                <xs:complexType>
                    <xs:sequence>
                        <xs:element name="KM" type="evidencedStringType" minOccurs="0" maxOccurs="unbounded"/>
                        <xs:element name="Vmax" type="evidencedStringType" minOccurs="0" maxOccurs="unbounded"/>
                        <xs:element name="text" type="evidencedStringType" minOccurs="0" maxOccurs="1"/>
                    </xs:sequence>
                </xs:complexType>
            </xs:element>
            <xs:element name="phDependence" type="evidencedStringType" minOccurs="0" maxOccurs="1"/>
            <xs:element name="redoxPotential" type="evidencedStringType" minOccurs="0" maxOccurs="1"/>
            <xs:element name="temperatureDependence" type="evidencedStringType" minOccurs="0" maxOccurs="1"/>
        </xs:sequence>
    </xs:group>

Not before: 02-Mar-2010

UniProtKB entries no longer describe proteins of several organisms. We will adapt the XSD in the following way:

• Change the cardinality of the organism element to 1.
• Remove the species element from the XSD type sourceDataType.
• Add a new optional evidence attribute to the organism element and remove the key attribute.

    <xs:element name="entry">
    ...
    <xs:complexType name="sourceDataType">
        <xs:choice maxOccurs="unbounded">
            <!-- 
            <<xs:element name="species">
                <xs:complexType>
                    <xs:simpleContent>
                        <xs:extension base="xs:string">
                            <xs:attribute name="ref" type="xs:string" use="optional"/>
                        </xs:extension>
                    </xs:simpleContent>
                </xs:complexType>
            </xs:element>
            -->
            <xs:element name="strain">
            ...
    ...
    <xs:complexType name="organismType">
        ...
   <!-- <xs:attribute name="key" type="xs:string" use="required"/> -->
        <xs:attribute name="evidence" type="xs:string" use="optional"/>
    </xs:complexType>
    ...
           <!-- <xs:element name="organism" type="organismType" maxOccurs="unbounded"/> -->
                <xs:element name="organism" type="organismType"/>

Not before: 02-Mar-2010

For reasons of consistency, we are going to do the following changes:

• Change the casing of the element CdAntigenName to cdAntigenName:

      <xs:group name="proteinNameGroup">
          <xs:sequence>
              ...
              <xs:element name="cdAntigenName" type="evidencedStringType" minOccurs="0" maxOccurs="unbounded"/>
  

• Change the casing of the enumeration values of the type attribute of the XSD type proteinExistenceType:

      <xs:complexType name="proteinExistenceType">
          <xs:attribute name="type" use="required">
             <xs:simpleType>
                  <xs:restriction base="xs:string">
                      <xs:enumeration value="evidence at protein level"/>
                      <xs:enumeration value="evidence at transcript level"/>
                      <xs:enumeration value="inferred from homology"/>
                      <xs:enumeration value="predicted"/>
                      <xs:enumeration value="uncertain"/>
  

• Change the casing of the enumeration values of the status attribute of the XSD type evidencedStringType:

      <xs:complexType name="evidencedStringType">
          ...
                  <xs:attribute name="status" use="optional">
                      <xs:simpleType>
                          <xs:restriction base="xs:string">
                              <xs:enumeration value="by similarity"/>
                              <xs:enumeration value="probable"/>
                              <xs:enumeration value="potential"/>
  

• Restrict the values of the status attribute of the XSD type featureType:

      <xs:complexType name="featureType">
          ...
     <!-- <xs:attribute name="status" type="xs:string" use="optional"/> -->
          <xs:attribute name="status" use="optional">
              <xs:simpleType>
                  <xs:restriction base="xs:string">
                      <xs:enumeration value="by similarity"/>
                      <xs:enumeration value="probable"/>
                      <xs:enumeration value="potential"/>
                  </xs:restriction>
              </xs:simpleType>
          </xs:attribute>
  

Not before: 23-Mar-2010

Two new event types are going to be added to the comment line topic ALTERNATIVE PRODUCTS in the flat file format of UniProtKB entries. For details of this change, please read the UniProt document Forthcoming changes.

To represent this data in the XML format, we are going to modify the XSD type eventType in the following way:

     <xs:complexType name="eventType">
     ...
         <xs:attribute name="type" use="required">
         ...
                     <xs:enumeration value="protein splicing"/>
                     <xs:enumeration value="miscellaneous"/>